Hepatitis C virus population analysis of a single-source nosocomial outbreak reveals an inverse correlation between viral load and quasispecies complexity Antonio Mas, 1 Encarna Ulloa, 1 Miguel Bruguera, 2 Ivana Furc ˇic ´, 2 3 Damia ` Garriga, 1 4 Silvia Fa ´ bregas, 3 David Andreu, 1 Juan Carlos Saiz 4 and Juana Dı ´ez 1 Correspondence Juana Dı ´ez juana.diez@upf.edu 1 Departamento de Ciencias Experimentales y de la Salud, Universitat Pompeu Fabra, Dr. Aiguader 80, 08003 Barcelona, Spain 2 Hepatologı ´a, Instituto de Enfermedades Digestivas, Hospital Clinic, 08036 Barcelona, Spain 3 Hospital Figueres, 17600 Girona, Spain 4 Departamento de Biotecnologı ´a, Instituto Nacional de Investigacio ´ n y Tecnologı ´a Agraria y Alimentaria, 28040 Madrid, Spain Received 3 August 2004 Accepted 25 August 2004 The features of Hepatitis C virus (HCV) quasispecies within an envelope segment including the hypervariable region 1 were analysed at an early time point post-infection in seven patients that acquired HCV from a single common donor during a nosocomial outbreak. The grouping of patients according to viral load was reflected in the structure of the quasispecies. A higher viral load correlated with the presence of a predominant HCV genome and a corresponding lower quasispecies complexity. The quasispecies complexity itself was not correlated with HCV clearance or persistence. Thus, the relationship between an intrapatient HCV quasispecies and the clinical outcome of an HCV infection is more complex than previously anticipated. INTRODUCTION Hepatitis C virus (HCV) is an enveloped positive-strand RNA virus of the family Flaviviridae. Only about 15–30 % of HCV infections are spontaneously cleared, the remain- ing result in virus persistence with subsequent develop- ment of chronic hepatitis, liver cirrhosis and hepatocellular carcinoma (Alter et al., 1999). Because worldwide over 170 million people are infected carriers, HCV is a major health problem and a key issue in antiviral research. The mechanisms responsible for the high rate of viral persistence are thought to be the result of a complex host–virus interaction early after infection (Racanelli & Rehermann, 2003). However, little is known about these early virus and host determinants because the acute phase of infection is often asymptomatic and thus most diagnoses are made during the chronic stage, i.e. months or years after the events that determined the clinical course of the infec- tion. While HCV induces strong humoral and cellular immune responses, their roles in virus clearance or persis- tence have not been fully elucidated. Studies in humans and chimpanzees indicate that a robust intrahepatic CD4 + and CD8 + T-cell response during the first weeks after infection is associated with viral clearance (Cooper et al., 1999; Major et al., 2004; Thimme et al., 2002). Also, antibodies may play a role here because an early antibody recognition of the hypervariable region 1 (HVR1) in the envelope E2 protein was correlated with virus clearance (Allander et al., 1997), and infection of chimpanzees could be inhibited by a human hyperimmune serum against HVR1 (Farci et al., 1996). In line with this are studies on the rate of HVR1 evolution that have suggested that the HVR1 region is under immune pressure exerted by neutralizing antibodies (Booth et al., 1998; Kato et al., 1993; Shimizu et al., 1994; Weiner et al., 1992). Nevertheless, by using infectious retroviral pseudo- types, a recent study has shown that neutralizing antibody responses early after infection do not seem to play a role in the resolution of an acute infection (Logvinoff et al., 2004). What is the strategy of HCV to survive and establish per- sistence? This question is still unresolved. One interesting 3Present address: Department of Molecular Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, HR-10000 Zagreb, Croatia. 4Present address: Departament de Biologia Estructural, Institut de Biologia Molecular de Barcelona (CSIC), Josep Samitier 1-5, 08028 Barcelona, Spain. The GenBank/EMBL/DDBJ accession numbers of the nucleotide sequences reported here are AY683898–AY684043. 0008-0500 G 2004 SGM Printed in Great Britain 3619 Journal of General Virology (2004), 85, 3619–3626 DOI 10.1099/vir.0.80500-0